Well thanks to my kind folk over at Server Fault, I now have a solution as to why dnscmd suddenly stopped working. It would turn out that the strange behaviour I was seeing was a result of a Microsoft implementation of handling 32bit running on 64bit (WoW64) Operating systems.
Specifically, it was caused by Filesystem Redirection
However, I found that trying to user %windir%\sysnative did not work for me in my powershell console. That’s odd, so I did a bit more research. A post over at Nynaeve got me on the right track.